Journal of microbiological methods最新文献_第3页

The bacterial endotoxin test in the Chinese pharmacopoeia: A journey of international harmonization and national consideration 《中国药典》细菌内毒素检查法：国际统一与国内思考之旅

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-29 DOI: 10.1016/j.mimet.2026.107411

Tong Cai, Yusheng Pei

{"title":"The bacterial endotoxin test in the Chinese pharmacopoeia: A journey of international harmonization and national consideration","authors":"Tong Cai, Yusheng Pei","doi":"10.1016/j.mimet.2026.107411","DOIUrl":"10.1016/j.mimet.2026.107411","url":null,"abstract":"<div><div>The Bacterial Endotoxin Test (BET) is a critical quality control measure for parenteral drugs and sterile medical devices worldwide. As the global pharmaceutical industry becomes increasingly integrated, the harmonization of pharmacopoeial methods is an inevitable trend. The Chinese Pharmacopoeia (ChP), China's official national standard, has undergone significant evolution in its BET chapter, transitioning from initially referencing the United States Pharmacopoeia (USP) to progressively aligning with the International Council for Harmonization (ICH) Harmonized Tripartite Guideline:Evaluation and Recommendation of Pharmacopoeial Texts for Use in The ICH Regions on Bacterial Endotoxin Test General Chapter Q4B (ICH Q4B).</div><div>This article provides a comprehensive overview of the development of the BET in the ChP, with a special focus on the major revisions in the newly implemented 2025 edition. We detail how the ChP 2025 further converges with the ICH harmonized text in aspects such as method classification, procedural descriptions, and key validation parameters. Concurrently, we elucidate the scientific rationale for retaining specific “Chinese characteristics,” such as stricter requirements for water for BET, a different standard for average body weight in limit calculations, and more stringent retest protocols for the gel-clot method, all of which are rooted in domestic regulatory practices and public health considerations. Furthermore, we discuss China's proactive approach to addressing emerging global challenges like Low Endotoxin Recovery (LER) and its pioneering research into resource-saving micro-methods. This review aims to offer international stakeholders a clear perspective on the scientific rigor, commitment to global standards, and unique risk-based considerations that define the modern BET in China.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107411"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146080332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Automatic colony cell counting method of phytoplankton in microscopic images with multi-task learning 基于多任务学习的浮游植物显微图像集落细胞自动计数方法。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-20 DOI: 10.1016/j.mimet.2026.107396

Renqing Jia , Gaofang Yin , Nanjing Zhao , Min Zhang , Chao Zhu , Tianhong Liang , Jingze Zhang , Changbiao Yuan , Jiamin Tao , Peng Yun

{"title":"Automatic colony cell counting method of phytoplankton in microscopic images with multi-task learning","authors":"Renqing Jia , Gaofang Yin , Nanjing Zhao , Min Zhang , Chao Zhu , Tianhong Liang , Jingze Zhang , Changbiao Yuan , Jiamin Tao , Peng Yun","doi":"10.1016/j.mimet.2026.107396","DOIUrl":"10.1016/j.mimet.2026.107396","url":null,"abstract":"<div><div>Phytoplankton are key bioindicators in aquatic ecosystems, where species distribution and cell abundance serve as vital metrics for environmental assessment. Although image-based automated identification has progressed, accurately counting colonial cells remains challenging. This paper proposes a novel method for simultaneous phytoplankton recognition and cell counting. Using ResNet50 as a backbone, deep features are extracted from microscopic images of algal colonies. These features are then fed into two parallel branches for classification and counting, respectively, with model parameters updated through alternating training. Evaluated on 16 common colonial algae species from Lake Chaohu, the proposed method achieved 99.2% identification accuracy, 93.9% average counting accuracy, with mean absolute error and mean squared error of 1.290 and 2.263, respectively. This method effectively overcomes the challenges associated with colonial phytoplankton by integrating both identification and counting into a unified framework, providing a robust tool for automated aquatic algal monitoring.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107396"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146029936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improved RNA extraction from Pseudomonas aeruginosa biofilms using a lysozyme-modified commercial kit 利用溶菌酶修饰的商用试剂盒改进铜绿假单胞菌生物膜中RNA的提取。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-02-02 DOI: 10.1016/j.mimet.2026.107417

May M. Alrashed , Abdurahman A. Niazy , Rhodanne Nicole A. Lambarte , Amani A. Niazy

引用次数: 0

Plant-based dyes as eco-friendly alternative for visualization of arbuscular mycorrhizal fungi 植物基染料作为可视化丛枝菌根真菌的环保替代品。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-02-01 DOI: 10.1016/j.mimet.2026.107416

Bappa Karmakar, Mahasweta Chakraborty

引用次数: 0

FastqOrienter: A Python utility for the automated orientation and quality diagnostics of paired-end Illumina metabarcoding reads FastqOrienter：一个Python实用程序，用于对成对的Illumina元条形码读取进行自动定位和质量诊断。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-30 DOI: 10.1016/j.mimet.2026.107413

Daniele De Luca

引用次数: 0

Advancing pleural effusion diagnosis: Application of Molecular Culture ID in pathogen detection 推进胸腔积液诊断：分子培养ID在病原体检测中的应用。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-03-01 Epub Date: 2026-01-15 DOI: 10.1016/j.mimet.2026.107395

Lauren Remijas , Martine P. Bos , María Miguélez Sánchez , Robin van Houdt , Gernot Rohde , Andries E. Budding

{"title":"Advancing pleural effusion diagnosis: Application of Molecular Culture ID in pathogen detection","authors":"Lauren Remijas , Martine P. Bos , María Miguélez Sánchez , Robin van Houdt , Gernot Rohde , Andries E. Budding","doi":"10.1016/j.mimet.2026.107395","DOIUrl":"10.1016/j.mimet.2026.107395","url":null,"abstract":"<div><div>The diagnosis of pleural infection has traditionally relied on microbiological culture, a method often limited by slow bacterial growth and difficulties in culturing fastidious organisms. This study introduces Molecular Culture ID, a rapid and comprehensive molecular technique capable of detecting and identifying a wide range of bacteria down to the species level. By analyzing 440 pleural effusion samples derived from patients suspected of pleural infection and comparing the outcome to routine diagnostics, we demonstrate that Molecular Culture ID significantly outperforms traditional culture. Molecular Culture ID identified 133 positive samples, compared to 55 positive samples identified by traditional culture. The 78 additional positive samples detected by Molecular Culture contained important pathogens including species such as <em>Streptococcus pneumoniae, Escherichia coli</em>, and <em>Staphylococcus aureus</em>. These findings highlight Molecular Culture ID as a promising alternative for the rapid and accurate diagnosis of pleural infections, offering a substantial improvement over conventional methods.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107395"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145994335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Roadmap for emerging antimicrobial susceptibility testing and its clinical adaptation, from bench to bedside 新兴的抗菌药物敏感性测试及其临床适应性路线图，从实验室到床边

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-02-01 Epub Date: 2026-01-01 DOI: 10.1016/j.mimet.2025.107386

Pradhapsingh Bharathiraja, Elavarasan Tamilmani

{"title":"Roadmap for emerging antimicrobial susceptibility testing and its clinical adaptation, from bench to bedside","authors":"Pradhapsingh Bharathiraja, Elavarasan Tamilmani","doi":"10.1016/j.mimet.2025.107386","DOIUrl":"10.1016/j.mimet.2025.107386","url":null,"abstract":"<div><div>The rapid emergence of antimicrobial resistance (AMR) underscores the urgent need for accurate and timely antimicrobial susceptibility testing (AST) to guide effective antibiotic treatment. Currently, various AST techniques have evolved, however, no single, globally adopted rapid diagnostic technology available for AST diagnosis. Disk diffusion remains a widely accepted technique around the world for AST detection, despite its limitations and ineffective antibiotic efficacy. Regardless of antimicrobial stewardship program, these delayed diagnosis lead to the overuse of broad-spectrum antibiotics to primarily treat the infections and contribute to AMR development. Although automated AST systems offer improved sensitivity and effective in rapid diagnosis, their limited accessibility in low-resource settings and expensive test cost hinders its widespread adaptation. Emerging innovative AST technologies show promise in point-of-care testing but require validation and integration into clinical workflows. Clinical AST market demands differentiated solutions like high-throughput automation for well-resourced settings and affordable semi-automated solutions for low-resource healthcare areas. Therefore, this review extensively addresses the integration of existing AST technologies with emerging techniques, the key challenges in development, regulatory compliance, and clinical implementation. Additionally, highlight the urgent need for next-generation semi-automated AST technology to balance efficacy and affordability for improving individual patient outcomes in the global fight against AMR.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107386"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145881352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial community analyses of composts are influenced by particle size fraction and DNA extraction method 堆肥的微生物群落分析受颗粒大小、组分和DNA提取方法的影响

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-02-01 Epub Date: 2026-01-13 DOI: 10.1016/j.mimet.2025.107384

Anja Logo , Tabea Koch , Monika Maurhofer , Thomas Oberhänsli , Barbara Thürig , Franco Widmer , Pascale Flury , Johanna Mayerhofer

{"title":"Microbial community analyses of composts are influenced by particle size fraction and DNA extraction method","authors":"Anja Logo , Tabea Koch , Monika Maurhofer , Thomas Oberhänsli , Barbara Thürig , Franco Widmer , Pascale Flury , Johanna Mayerhofer","doi":"10.1016/j.mimet.2025.107384","DOIUrl":"10.1016/j.mimet.2025.107384","url":null,"abstract":"<div><div>Composting plays a key role in sustainable agriculture by converting organic waste into a valuable soil conditioner. The process is driven by complex microbial communities, whose characterization is essential for optimizing the composting process and compost quality. Molecular techniques such as amplicon sequencing are commonly used for this purpose. However, sampling procedures and DNA extraction methods, key steps in the sequencing workflow, often vary across studies, challenging comparability. We investigated two aspects of sample preparation that may influence compost microbial analyses. For DNA extraction, often fine fractions (<2 mm) are used. However, compost has a heterogeneous structure, including coarse particles. To assess the effect of particle size, we separately sequenced bacterial and fungal communities of the fine (0–2 mm) and coarse (2–10 mm) fractions of three composts. In addition, DNA was extracted using a carboxyl-affinity-based magnetic method and a silanol-affinity-based filter method to evaluate the impact of the extraction technique. We found that the coarse fraction had higher bacterial richness and distinct bacterial and fungal community structures compared to the fine fraction. DNA extraction method also influenced bacterial community profiles, with the magnetic bead method improving coverage, particularly for <em>Bacillota</em>. Although the effects of particle size and extraction method were small compared to the overall diversity among composts, we recommend including coarse particles in sequencing analyses and using standardized DNA extraction protocols, especially for studies aiming at high-resolution community analyses.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107384"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145978485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Developing machine learning classifiers for carbapenem resistance prediction in Klebsiella pneumoniae using Google's teachable machine 利用谷歌的可教机器开发肺炎克雷伯菌碳青霉烯类耐药性预测的机器学习分类器

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-02-01 Epub Date: 2025-12-31 DOI: 10.1016/j.mimet.2025.107385

João V.O. Cruz , Felipe G. Sacoda , Vitor H. Moreau , Luis G.C. Pacheco

引用次数: 0

Identification and characterization of cephalosporin-resistant Klebsiella pneumoniae by SERS: Insights into antimicrobial resistance patterns SERS鉴定和表征耐头孢菌素肺炎克雷伯菌：对抗菌药物耐药模式的见解。

IF 1.9 4区生物学

Journal of microbiological methods Pub Date : 2026-02-01 Epub Date: 2025-12-31 DOI: 10.1016/j.mimet.2025.107388

Benish Saif , Zainab Iftikhar , Haq Nawaz , Muhammad Irfan Majeed , Mashkoor Mohsin , Rabia Saleem , Najah Alwadie , Sundas Sakhawat , Kinza Khan , Aleena Ali , Rimsha Khan , Riha Zulfiqar , Amna Sattar , Muhammad Imran

{"title":"Identification and characterization of cephalosporin-resistant Klebsiella pneumoniae by SERS: Insights into antimicrobial resistance patterns","authors":"Benish Saif , Zainab Iftikhar , Haq Nawaz , Muhammad Irfan Majeed , Mashkoor Mohsin , Rabia Saleem , Najah Alwadie , Sundas Sakhawat , Kinza Khan , Aleena Ali , Rimsha Khan , Riha Zulfiqar , Amna Sattar , Muhammad Imran","doi":"10.1016/j.mimet.2025.107388","DOIUrl":"10.1016/j.mimet.2025.107388","url":null,"abstract":"<div><div>The infectious bacteria, <em>K. pneumoniae</em> has broken another defence line by showing resistance to cephalosporin antibiotics, due to presence of extended-spectrum lactamases ESBL resistance genes. Surface-enhanced Raman spectroscopy (SERS) is used to characterize third generation cephalosporin resistant and susceptible <em>K. pneumoniae</em> strains for the purpose of identification of their characteristic SERS spectral features. For this, the silver nanoparticles (Ag-NPs) are used as a SERS substrate. The SERS spectral fingerprints of <em>K. pneumoniae</em> strains, linked directly or indirectly to resistance development against third generation cephalosporins, were differentiated by analyzing their SERS spectral data with the help of support vector machines (SVM), principal component analysis (PCA), and partial least squares discriminant analysis (PLS-DA). This can result in the effective recognition, differentiation and distinction of third generation cephalosporin resistant and susceptible strains of <em>K. pneumonia</em> bacteria which is considered crucial for selecting suitable antibiotic treatment for infections<em>.</em></div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107388"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0